Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate GFF2490 PS417_12700 ABC transporter ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__WCS417:GFF2490 Length = 367 Score = 310 bits (794), Expect = 4e-89 Identities = 178/375 (47%), Positives = 239/375 (63%), Gaps = 24/375 (6%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M LK+ N+ K + ++ +L+++DKEF+VFVGPSGCGKST LR+IAGLE+++EG Sbjct: 1 MANLKIKNLQKGFEGFS--IIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEG 58 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 + +D + + + +P RD+AMVFQ YALYPHMSV +NM+F L L K + +V EAA Sbjct: 59 TIELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAA 118 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 IL L LERKP LSGGQRQRVA+GRAIVR+ K+FL DEPLSNLDA LRV MR E+A+ Sbjct: 119 RILELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELAR 178 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 +H+ + AT IYVTHDQ EAMTLAD++V++++ GRIEQ+G+P ELY++PAN Sbjct: 179 LHKELQATMIYVTHDQVEAMTLADKVVVLNS----------GRIEQVGSPLELYHQPANL 228 Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKG---YLGKKVTLGIRP 297 FVAGF+G+P M F + V + V + L G L G +G VTLGIRP Sbjct: 229 FVAGFLGTPKMGFLKGKVTR---VESQSCEVQLDAGTLINLPLSGATLSVGSAVTLGIRP 285 Query: 298 EDISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTE-FTARVNARDSHSPGEKV 356 E + +I +VTAD V E LGS++ +V + E T R+ + GE + Sbjct: 286 EHL---EIASPGQTTLTVTAD--VGERLGSDTFCHVITANGEPLTMRIRGDMASQYGETL 340 Query: 357 QLTFNIAKGHFFDLE 371 L + A H FD + Sbjct: 341 HLHLDPAHCHLFDTD 355 Lambda K H 0.318 0.135 0.379 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 317 Number of extensions: 11 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 377 Length of database: 367 Length adjustment: 30 Effective length of query: 347 Effective length of database: 337 Effective search space: 116939 Effective search space used: 116939 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory